Inferring the effect of species interactions on trait evolution
Data files
Sep 09, 2020 version files 2.91 GB
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abundance_test.rar
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BaleenWhaleData&Results.rar
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Estimation.rar
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PredictionDis.rar
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SimEstResults.rar
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SimTreeInfo.rar
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smc_traittrees.rar
Dec 03, 2020 version files 2.92 GB
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abundance_test.rar
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BaleenWhaleData&Results.rar
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Estimation.rar
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PredictionDis.rar
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SimEstResults.rar
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SimTreeInfo.rar
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smc_traittrees.rar
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Supplementary_material_of_Inferring_the_effect_of_species_interactions_on_trait_evolution.pdf
Abstract
Methods
The derivation of the model is in Supplementary_material_of_Inferring_the_effect_of_species_interactions_on_trait_evolution.pdf in the attachments.
Usage notes
Supplementary results
Figures S2-S16. Trait trees under different parameter combinations of Scenarios 1, 2, 3 under the AWC model and the UWC model for the tree values of scaling parameters, s=100,1000,10000. For the figures of the rest of the secenarios, they are stored in the folder “abundance_test.”
Figures S17-S18. Trait trees under different parameter combinations of different scenarios.
Figures S19-S21. Prediction of the abundance distribution versus body length across 1000 simulations using the estimated parameters for Scenarios 1-3. For the figures of the rest of the scenarios, they are stored in the folder “PredictionDis.”
Figures S22-S24. Predictions of the trait variance distribution across 100 simulations using the estimated parameters for Scenarios 1-3. For the figures of the rest of the scenarios, they are stored in the folder “PredictionDis.”
Figures S25-S27. Comparison of the parameter estimates for those generating parameters for which the ratio \frac{\sqrt{\alpha/\gamma}}{\text{Richness}} is in the range of (0.5,1.5). The figures of other scenarios are stored in the folder “Estimation.”
Figures S28-S58. Comparison of the estimates among different scenarios.
Figures S59-S60. Parameter estimates under PICs and UMTD+PICs for the AWC model on the logtransformed body length.
Figures S61-S63. Parameter estimates under SMTD, PICs and UMTD+PICs for the AWC model on the untransformed body length.
Figures S64-S66. Results of the model comparison analysis on the untransformed body length.
Figures S67-S69. Results of the model comparison analysis on the logtransformed body length.
Figure S70. Abundance distributions of the AWC and MWC models.
Figure S71. Trait variance distributions of the AWC and MWC models.
Figures S72-74. Distribution of the goodness-of-fit of the three models using three summary statistics. The red dashed line represents the 5% best GOF-values.
Figure S75. The predicted contrasts using the estimated parameters under the three models and the true contrasts for PICs.
Figure S76. The predicted contrasts using the estimated parameters under the three models and the true contrasts for UMTD+PICs.
Phylogenetic tree data for Scenarios 1-22. They are stored in the folder “SimTreeInfo” and indexed accordingly.
All the data of generated trees used in the simulation study (Scenarios 1-22) are stored in the folder “SimTreeInfo.”
The inference results of the simulation study are stored in the folder “SimEstResults.”
The baleen whale data and results are stored in the folder “BaleenWhaleData&Results.”